I would imagine every city with a major coastal or inland airport like NYC or LA or Atlanta would prime choices for a Nintendo store.
Anyway, Ian, since it would be a Nintendo store owned by Nintendo and whatnot, they would not need to worry about contract gabbledegook with EB for demo units AND would not have to worry much about competitor vandalism, like what happened during the Xbox/GC launch. Also, demos and stuff would get there sooner because it would come directly from the source. Imagine being able to play the E3 demo of everything at anytime since Nintendo would just keep those discs from E3 and use them in the store.